|
| Status |
Public on May 13, 2013 |
| Title |
OCI-Ly7 scrambled |
| Sample type |
SRA |
| |
|
| Source name |
OCI-Ly7 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: OCI-Ly7 cell line
treatment: transuced with control scrambled shRNA for 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturer’s protocol.
ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iTâ„¢ dsDNA HS Assay (Life Technologies)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
genome build: hg19
Illumina Casava1.8 software used for basecalling.
RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml)
|
| |
|
| Submission date |
Apr 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Matt Teater |
| E-mail(s) |
mrt2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Street address |
445 E 69th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE45982 |
EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation |
|
| Relations |
| BioSample |
SAMN02056266 |
| SRA |
SRX271817 |
